The statistical properties of molecular genetic variation within populations will be examined by theoretical analysis and computer simulation. Methods of estimating the recombination rate in different regions of the genome will be developed and evaluated. Two different statistical tests of the neutral model will be investigated. A test of heterogeneity of mutation parameters will also be developed. These statistical investigations will provide important tools for the analysis of the great quantity of DNA sequence data which is now becoming available. These statistical tools together with the new data will permit significant progress on questions concerning genetic variation in populations, including molecular genetic variation in human populations. These statistical tools may be very useful for the understanding of molecular genetic variation associated with genetic disease in humans. The models to be studied include a selectively neutral model with constant population size, a neutral model with varying population size, and a neutral model with population subdivision. Also considered will be a model with strong balancing selection and a model with occasional occurrence of favorable mutations that sweep through the population.